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#!/bin/sh
#
# Downloads sequence for a D. melanogaster from flybase. Currently set
# to download 5.22, but F, REL, and IDX_NAME can be edited to reflect a
# different version number. (But note that you will usually also have
# to change the date in REL.)
#
GENOMES_MIRROR=ftp://ftp.flybase.net/genomes/Drosophila_melanogaster
F=dmel-all-chromosome-r5.48.fasta
REL=dmel_r5.48_FB2012_06
IDX_NAME=d_melanogaster_fb5_48
get() {
file=$1
if ! wget --version >/dev/null 2>/dev/null ; then
if ! curl --version >/dev/null 2>/dev/null ; then
echo "Please install wget or curl somewhere in your PATH"
exit 1
fi
curl -o `basename $1` $1
return $?
else
wget -O `basename $1` $1
return $?
fi
}
BOWTIE_BUILD_EXE=./bowtie2-build
if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
if ! which bowtie2-build ; then
echo "Could not find bowtie2-build in current directory or in PATH"
exit 1
else
BOWTIE_BUILD_EXE=`which bowtie2-build`
fi
fi
if [ ! -f $F ] ; then
FGZ=$F.gz
get ${GENOMES_MIRROR}/$REL/fasta/$FGZ || (echo "Error getting $FGZ" && exit 1)
gunzip $FGZ || (echo "Error unzipping $FGZ" && exit 1)
fi
CMD="${BOWTIE_BUILD_EXE} $* $F $IDX_NAME"
echo "Running $CMD"
if $CMD ; then
echo "$IDX_NAME index built; you may remove fasta files"
else
echo "Index building failed; see error message"
fi
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